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Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop

This commit is contained in:
Sandro La Bruzzo 2020-04-17 12:12:25 +02:00
parent 5e2fa996aa 09f356b047
commit 01ea7721f3
15 changed files with 154 additions and 47 deletions
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12
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
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@ -29,17 +29,21 @@ public class ISClient implements Serializable {
private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
public static List<String> getLatestRawsetPaths(String isLookupUrl, String setIds) {
private ISLookUpService isLookup;
public ISClient(String isLookupUrl) {
isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
}
public List<String> getLatestRawsetPaths(String setIds) {
ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
ISClient isClient = new ISClient();
List<String> ids = Lists.newArrayList(Splitter.on(INPUT_ACTION_SET_ID_SEPARATOR)
.omitEmptyStrings()
.trimResults()
.split(setIds));
return ids.stream()
.map(id -> isClient.getSet(isLookup, id))
.map(id -> getSet(isLookup, id))
.map(as -> as.getPathToLatest())
.collect(Collectors.toCollection(ArrayList::new));
}

36
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java
View File

@ -41,6 +41,15 @@ public class PartitionActionSetsByPayloadTypeJob {
StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty())
));
private ISClient isClient;
public PartitionActionSetsByPayloadTypeJob(String isLookupUrl) {
this.isClient = new ISClient(isLookupUrl);
}
public PartitionActionSetsByPayloadTypeJob() {
}
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils.toString(
PromoteActionPayloadForGraphTableJob.class
@ -63,7 +72,12 @@ public class PartitionActionSetsByPayloadTypeJob {
String isLookupUrl = parser.get("isLookupUrl");
logger.info("isLookupUrl: {}", isLookupUrl);
List<String> inputActionSetPaths = ISClient.getLatestRawsetPaths(isLookupUrl, inputActionSetIds);
new PartitionActionSetsByPayloadTypeJob(isLookupUrl).run(isSparkSessionManaged, inputActionSetIds, outputPath);
}
protected void run(Boolean isSparkSessionManaged, String inputActionSetIds, String outputPath) {
List<String> inputActionSetPaths = getIsClient().getLatestRawsetPaths(inputActionSetIds);
logger.info("inputActionSetPaths: {}", String.join(",", inputActionSetPaths));
SparkConf conf = new SparkConf();
@ -95,21 +109,15 @@ public class PartitionActionSetsByPayloadTypeJob {
String path) {
logger.info("Reading actions from path: {}", path);
List<String> files = HdfsSupport.listFiles(path, spark.sparkContext().hadoopConfiguration());
logger.info("Found files: {}", String.join(",", files));
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
return files
.stream()
.map(file -> {
JavaRDD<Row> rdd = sc
.sequenceFile(file, Text.class, Text.class)
.sequenceFile(path, Text.class, Text.class)
.map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
return spark.createDataFrame(rdd, KV_SCHEMA)
.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
.select(expr("atomic_action.*"));
})
.reduce(spark.createDataFrame(Collections.emptyList(), ATOMIC_ACTION_SCHEMA), Dataset::union);
}
private static void saveActions(Dataset<Row> actionDS,
@ -121,4 +129,12 @@ public class PartitionActionSetsByPayloadTypeJob {
.mode(SaveMode.Append)
.parquet(path);
}
public ISClient getIsClient() {
return isClient;
}
public void setIsClient(ISClient isClient) {
this.isClient = isClient;
}
}

8
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java
View File

@ -8,6 +8,7 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
@ -119,10 +120,17 @@ public class PromoteActionPayloadForGraphTableJob {
String path,
Class<G> rowClazz) {
logger.info("Reading graph table from path: {}", path);
return spark.read()
.textFile(path)
.map((MapFunction<String, G>) value -> OBJECT_MAPPER.readValue(value, rowClazz), Encoders.bean(rowClazz));
/*
return spark
.read()
.parquet(path)
.as(Encoders.bean(rowClazz));
*/
}
private static <A extends Oaf> Dataset<A> readActionPayload(SparkSession spark,

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml
View File

@ -118,6 +118,9 @@
<action name="SkipPromoteDatasetActionPayloadForDatasetTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${workingDir}/dataset"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/dataset</arg>
<arg>${workingDir}/dataset</arg>
@ -166,6 +169,9 @@
<action name="SkipPromoteResultActionPayloadForDatasetTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/dataset"/>
</prepare>
<arg>-pb</arg>
<arg>${workingDir}/dataset</arg>
<arg>${outputGraphRootPath}/dataset</arg>

3
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml
View File

@ -113,6 +113,9 @@
<action name="SkipPromoteDatasourceActionPayloadForDatasourceTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/datasource"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/datasource</arg>
<arg>${outputGraphRootPath}/datasource</arg>

3
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml
View File

@ -113,6 +113,9 @@
<action name="SkipPromoteOrganizationActionPayloadForOrganizationTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/organization"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/organization</arg>
<arg>${outputGraphRootPath}/organization</arg>

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml
View File

@ -117,6 +117,9 @@
<action name="SkipPromoteOtherResearchProductActionPayloadForOtherResearchProductTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${workingDir}/otherresearchproduct"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/otherresearchproduct</arg>
<arg>${workingDir}/otherresearchproduct</arg>
@ -165,6 +168,9 @@
<action name="SkipPromoteResultActionPayloadForOtherResearchProductTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/otherresearchproduct"/>
</prepare>
<arg>-pb</arg>
<arg>${workingDir}/otherresearchproduct</arg>
<arg>${outputGraphRootPath}/otherresearchproduct</arg>

3
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml
View File

@ -113,6 +113,9 @@
<action name="SkipPromoteProjectActionPayloadForProjectTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/project"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/project</arg>
<arg>${outputGraphRootPath}/project</arg>

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml
View File

@ -118,6 +118,9 @@
<action name="SkipPromotePublicationActionPayloadForPublicationTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${workingDir}/publication"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/publication</arg>
<arg>${workingDir}/publication</arg>
@ -166,6 +169,9 @@
<action name="SkipPromoteResultActionPayloadForPublicationTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/publication"/>
</prepare>
<arg>-pb</arg>
<arg>${workingDir}/publication</arg>
<arg>${outputGraphRootPath}/publication</arg>

3
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml
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@ -114,6 +114,9 @@
<action name="SkipPromoteRelationActionPayloadForRelationTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/relation"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/relation</arg>
<arg>${outputGraphRootPath}/relation</arg>

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml
View File

@ -117,6 +117,9 @@
<action name="SkipPromoteSoftwareActionPayloadForSoftwareTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${workingDir}/software"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/software</arg>
<arg>${workingDir}/software</arg>
@ -165,6 +168,9 @@
<action name="SkipPromoteResultActionPayloadForSoftwareTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/software"/>
</prepare>
<arg>-pb</arg>
<arg>${workingDir}/software</arg>
<arg>${outputGraphRootPath}/software</arg>

51
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java
View File

@ -1,6 +1,8 @@
package eu.dnetlib.dhp.actionmanager.partition;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.actionmanager.ISClient;
import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.hadoop.conf.Configuration;
@ -15,7 +17,11 @@ import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.types.*;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.api.io.TempDir;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;
import scala.Tuple2;
import scala.collection.mutable.Seq;
@ -31,6 +37,7 @@ import static org.apache.spark.sql.functions.*;
import static org.junit.jupiter.api.Assertions.assertIterableEquals;
import static scala.collection.JavaConversions.mutableSeqAsJavaList;
@ExtendWith(MockitoExtension.class)
public class PartitionActionSetsByPayloadTypeJobTest {
private static final ClassLoader cl = PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader();
@ -64,20 +71,29 @@ public class PartitionActionSetsByPayloadTypeJobTest {
@Nested
class Main {
@Mock
private ISClient isClient;
@Test
public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception {
// given
Path inputActionSetsDir = workingDir.resolve("input").resolve("action_sets");
Path inputActionSetsBaseDir = workingDir.resolve("input").resolve("action_sets");
Path outputDir = workingDir.resolve("output");
Map<String, List<String>> oafsByClassName = createActionSets(inputActionSetsDir);
Map<String, List<String>> oafsByClassName = createActionSets(inputActionSetsBaseDir);
List<String> inputActionSetsPaths = resolveInputActionSetPaths(inputActionSetsBaseDir);
// when
PartitionActionSetsByPayloadTypeJob.main(new String[]{
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-inputActionSetPaths", inputActionSetsDir.toString(),
"-outputPath", outputDir.toString()
});
Mockito.when(isClient.getLatestRawsetPaths(Mockito.anyString())).thenReturn(inputActionSetsPaths);
PartitionActionSetsByPayloadTypeJob job = new PartitionActionSetsByPayloadTypeJob();
job.setIsClient(isClient);
job.run(
Boolean.FALSE,
"", // it can be empty we're mocking the response from isClient to resolve the paths
outputDir.toString()
);
// then
Files.exists(outputDir);
@ -94,10 +110,19 @@ public class PartitionActionSetsByPayloadTypeJobTest {
}
}
private List<String> resolveInputActionSetPaths(Path inputActionSetsBaseDir) throws IOException {
Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
return Files
.list(inputActionSetJsonDumpsDir)
.map(path -> {
String inputActionSetId = path.getFileName().toString();
return inputActionSetsBaseDir.resolve(inputActionSetId).toString();
})
.collect(Collectors.toCollection(ArrayList::new));
}
private static Map<String, List<String>> createActionSets(Path inputActionSetsDir) throws IOException {
Path inputActionSetJsonDumpsDir = Paths
.get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/"))
.getFile());
Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
Map<String, List<String>> oafsByType = new HashMap<>();
Files
@ -138,6 +163,12 @@ public class PartitionActionSetsByPayloadTypeJobTest {
return oafsByType;
}
private static Path getInputActionSetJsonDumpsDir() {
return Paths
.get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/"))
.getFile());
}
private static Dataset<String> readActionsFromJsonDump(String path) {
return spark
.read()

6
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java
View File

@ -64,6 +64,7 @@ public class DispatchEntitiesApplication {
log.info(String.format("Processing entities (%s) in file: %s", type, sourcePath));
/*
spark.read()
.textFile(sourcePath)
.filter((FilterFunction<String>) value -> isEntityType(value, type))
@ -73,14 +74,13 @@ public class DispatchEntitiesApplication {
.mode(SaveMode.Overwrite)
.parquet(targetPath + "/" + type);
/*
*/
JavaSparkContext.fromSparkContext(spark.sparkContext())
.textFile(sourcePath)
.filter(l -> isEntityType(l, type))
.map(l -> StringUtils.substringAfter(l, "|"))
.saveAsTextFile(targetPath + "/" + type, GzipCodec.class); // use repartition(XXX) ???
*/
}
private static boolean isEntityType(final String line, final String type) {

10
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java
View File

@ -100,16 +100,24 @@ public class MergeClaimsApplication {
return opRaw.isPresent() ? opRaw.get()._2() : opClaim.isPresent() ? opClaim.get()._2() : null;
}, Encoders.bean(clazz))
.filter(Objects::nonNull)
.map((MapFunction<T, String>) value -> OBJECT_MAPPER.writeValueAsString(value), Encoders.STRING())
.write()
.mode(SaveMode.Overwrite)
.parquet(outPath);
.option("compression", "gzip")
.text(outPath);
}
private static <T extends Oaf> Dataset<T> readFromPath(SparkSession spark, String path, Class<T> clazz) {
return spark.read()
.textFile(path)
.map((MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz))
.filter((FilterFunction<T>) value -> Objects.nonNull(idFn().apply(value)));
/*
return spark.read()
.load(path)
.as(Encoders.bean(clazz))
.filter((FilterFunction<T>) value -> Objects.nonNull(idFn().apply(value)));
*/
}
private static void removeOutputDir(SparkSession spark, String path) {

32
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
View File

@ -10,6 +10,10 @@
<value>false</value>
<description>should import content from the aggregator or reuse a previous version</description>
</property>
<property>
<name>contentPath</name>
<description>path location to store (or reuse) content from the aggregator</description>
</property>
<property>
<name>postgresURL</name>
<description>the postgres URL to access to the database</description>
@ -108,10 +112,10 @@
<action name="ImportDB_claims">
<java>
<prepare>
<delete path="${workingDir}/db_claims"/>
<delete path="${contentPath}/db_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${workingDir}/db_claims</arg>
<arg>-p</arg><arg>${contentPath}/db_claims</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
@ -124,10 +128,10 @@
<action name="ImportODF_claims">
<java>
<prepare>
<delete path="${workingDir}/odf_claims"/>
<delete path="${contentPath}/odf_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${workingDir}/odf_claims</arg>
<arg>-p</arg><arg>${contentPath}/odf_claims</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
@ -141,10 +145,10 @@
<action name="ImportOAF_claims">
<java>
<prepare>
<delete path="${workingDir}/oaf_claims"/>
<delete path="${contentPath}/oaf_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${workingDir}/oaf_claims</arg>
<arg>-p</arg><arg>${contentPath}/oaf_claims</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>
@ -158,10 +162,10 @@
<action name="ImportDB">
<java>
<prepare>
<delete path="${workingDir}/db_records"/>
<delete path="${contentPath}/db_records"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${workingDir}/db_records</arg>
<arg>-p</arg><arg>${contentPath}/db_records</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
@ -173,10 +177,10 @@
<action name="ImportODF">
<java>
<prepare>
<delete path="${workingDir}/odf_records"/>
<delete path="${contentPath}/odf_records"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${workingDir}/odf_records</arg>
<arg>-p</arg><arg>${contentPath}/odf_records</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
@ -190,10 +194,10 @@
<action name="ImportOAF">
<java>
<prepare>
<delete path="${workingDir}/oaf_records"/>
<delete path="${contentPath}/oaf_records"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${workingDir}/oaf_records</arg>
<arg>-p</arg><arg>${contentPath}/oaf_records</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>
@ -227,7 +231,7 @@
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-s</arg><arg>${workingDir}/db_claims,${workingDir}/oaf_claims,${workingDir}/odf_claims</arg>
<arg>-s</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg>
<arg>-t</arg><arg>${workingDir}/entities_claim</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
@ -276,7 +280,7 @@
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-s</arg><arg>${workingDir}/db_records,${workingDir}/oaf_records,${workingDir}/odf_records</arg>
<arg>-s</arg><arg>${contentPath}/db_records,${contentPath}/oaf_records,${contentPath}/odf_records</arg>
<arg>-t</arg><arg>${workingDir}/entities</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>